MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : dctp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b1478 b1241 b4069 b4384 b2297 b2458 b2926 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b0261 b2799 b3945 b1602 b2342 b3845 b2913 b4381 b2406 b3915 b0529 b2492 b0904 b1380 b3662 b0606 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.351012 (mmol/gDw/h)
  Minimum Production Rate : 1.155195 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 34.186121
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.258454
  EX_pi_e : 3.804174
  EX_so4_e : 0.088392
  EX_k_e : 0.068515
  EX_fe3_e : 0.005638
  EX_mg2_e : 0.003045
  EX_ca2_e : 0.001827
  EX_cl_e : 0.001827
  EX_cu2_e : 0.000249
  EX_mn2_e : 0.000243
  EX_zn2_e : 0.000120
  EX_ni2_e : 0.000113

Product: (mmol/gDw/h)
  EX_h2o_e : 54.268216
  EX_co2_e : 33.445886
  EX_h_e : 5.261620
  Auxiliary production reaction : 1.155195
  EX_glyclt_e : 0.669226
  EX_ac_e : 0.204355
  EX_ade_e : 0.000393
  DM_5drib_c : 0.000236
  DM_4crsol_c : 0.000078

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

Last updated: 21-Sep-2023
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